Genetic and phenotypic traits in livestock

Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle

The paper quantifies how gene expression and splicing QTL explain heritability in cattle traits using Bayesian methods across 16 tissues.

Accelerated matrix-vector multiplications for matrices involving genotype covariates with applications in genomic prediction

The paper develops optimized matrix-vector multiplication methods for genomic prediction, improving computational efficiency on GPUs and CPUs for large datasets.

Whole genome sequencing provides novel insights into the evolutionary history and genetic adaptations of reindeer populations in northern Eurasia

This study uses whole-genome sequencing to analyze reindeer populations, identifying genetic clusters and domestication events in northern Eurasia.

Indigenous cattle of Sri Lanka: Genetic and phylogeographic relationship with Zebu of Indus valley and South Indian origin

This study analyzes the genetic diversity and phylogeography of Sri Lankan cattle breeds, finding strong relationships with South Indian Hallikar cattle and significant taurine admixture in two breeds.

Potential of imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss)

This study evaluates the use of low-density SNP panels with imputation for genomic selection in rainbow trout to improve resistance to Flavobacterium columnare, finding comparable accuracy to high-density panels at lower cost.

A multiplexed plant-animal SNP array for selective breeding and species conservation applications

This paper evaluates a multiplexed plant-animal SNP array for diverse applications, showing high SNP performance across species and cost savings through pooling.

Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia

Ancient Mongolian aurochs genomes show sustained male introgression and a link to Hereford cattle, but no genetic signature in modern East Asian breeds.

Genetic structure and genome-wide association study of the traditional Kazakh horses

This study investigates the genetic structure and genome-wide associations of Kazakh horses, identifying SNPs linked to traits like size and weight.

The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations

This study examines how genomic selection affects allele frequencies and new mutations over fifty generations, finding that genomic selection leads to faster and larger changes in allele frequencies compared to pedigree selection.

Using large-scale whole-genome sequence data for single-step genomic predictions in maternal and terminal pig lines

This study evaluates the impact of using whole-genome sequence data for genomic predictions in pig lines, finding modest improvements in accuracy for maternal lines but mixed results for terminal lines.

DeepMap: A deep learning-based model with four-line code for prediction-based breeding in crops

DeepMap is a deep learning-based genomic prediction tool that outperforms existing models in predicting crop phenotypes using genotype data.

Dimensionality of genomic information and its impact on GWA and variant selection: a simulation study

This study simulates GWA and variant selection to determine optimal sample sizes and variant inclusion strategies based on genomic dimensionality and effective population size.

Genetic Screening Of Halothane Gene On Selected Philippine Native Pig Herds

This study screens the Halothane gene in Philippine Native Pig herds using MS-PCR to identify carriers of the Porcine Stress Syndrome mutation, finding 5.89% heterozygous carriers.

A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes

The paper introduces a flexible empirical Bayes method for multivariate multiple regression to improve prediction of multi-tissue gene expression from genotypes.

Hitchhiking of bactericidal/permeability-increasing protein-like gene with the fibromelanosis locus in Kadaknath black-bone-chicken

The paper identifies a selective sweep near the fibromelanosis locus in Kadaknath chickens, showing hitchhiking of the BPIL gene due to linkage with the Fm locus.

The role of relatedness within a neighborhood in plant-to-plant interaction: effect on height growth and rust damage in Populus nigra

The paper examines how local relatedness affects tree height and rust damage in Populus nigra, finding that incorporating relatedness into genomic models improves rust resistance predictions but has limited overall effect.

Genetic Association of PLAG1 Gene Variant 14:25015640G>T with Wither-Height in Pakistani Cattle

The paper investigates the association of the PLAG1 gene variant 14:25015640G>T with wither-height in Pakistani cattle using ARMS-PCR and PLINK, finding significant genetic linkage and an odds ratio of 3.85.

Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits

This study identifies the genetic architecture of acute hyperthermia resistance in rainbow trout and shows it is polygenic with no major genetic correlations to production traits.

Variance component estimates, phenotypic characterization, and genetic evaluation of bovine congestive heart failure in commercial feeder cattle

The paper estimates variance components, characterizes phenotypes, and evaluates genetic factors associated with bovine congestive heart failure in commercial feeder cattle.

Genetic architecture of individual meiotic crossover rate and distribution in a large Atlantic Salmon (Salmo salar) breeding population.

The paper investigates genetic variation in recombination rates and distribution in Atlantic Salmon, finding sex-specific heritability and genetic independence between male and female crossover patterns.

Genetic analysis of protein efficiency and its association with performance and meat quality traits under a protein-restricted diet

This paper estimates the heritability of protein efficiency in pigs under a protein-restricted diet and its genetic correlations with performance and meat quality traits.

The first crested duck genome reveals clues to genetic compensation and crest cushion formation

This study generates a chromosome-level genome of Chinese crested ducks, identifies genetic compensation mechanisms, and reveals the genetic basis of crest formation.

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

The paper reports whole genome sequencing and de novo assemblies of four Bos indicus breeds, identifying phenotypic and biological process-related genes compared to B. taurus.

Genetic profiling and in silico sequence analysis of CSN2 (beta-casein) and CSN3 (κ-casein) genes in the indian buffalo (Bubalus bubalis)

The paper characterizes the CSN2 and CSN3 genes in Indian buffalo, analyzes their protein properties, and compares their evolutionary relationship with other species.

Genetic variation in promoter region of the bovine LAP3 gene associated with estimated breeding values of milk production traits and clinical mastitis in dairy cattle

GbyE: A New Genome Wide Association and Prediction Model based on Genetic by Environmental Interaction

GbyE improves genome-wide association and prediction by leveraging genetic by environmental interactions, showing higher statistical power across multiple species and heritability levels.

Combining phenotypic and genomic data to improve prediction of binary traits

The paper improves prediction of binary traits by combining genomic and phenotypic data using a two-step statistical method that prioritizes phenotypic variables.

Optimal implementation of genomic selection in clone breeding programs - exemplified in potato: I. Effect of selection strategy, implementation stage, and selection intensity on short-term genetic gain

This study evaluates how genomic selection (GS) can improve genetic gain in clone breeding programs, showing that GS strategies outperform phenotypic selection and recommend specific implementation stages for potato breeding.

Size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle

This study evaluates how haplotype reference panel size and composition affect variant calling accuracy from low-pass sequencing in cattle, finding that breed-specific panels improve imputation accuracy.

Development of genomic markers associated to production traits in lumpfish (Cyclopterus lumpus)

This study identifies genomic markers linked to production traits in lumpfish, enabling the development of a SNP panel for selective breeding.